| 1. |
- Hellgren, Mikko, et al.
(författare)
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Virtual screening for ligands to human alcohol dehydrogenase 3
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Alcohol dehydrogenase 3 (ADH3) has been suggested a role in nitric oxide homeostasis due to its function as a S-nitrosoglutathione (GSNO) reductase. This has requested a modulator of the ADH3 activity for control of GSNO levels. Today virtual screenings are frequently used in drug discovery to dock and rank a large number of compounds. With molecular dockings of more than 40,000 compounds into the active site pocket of human ADH3 we ranked compounds with a novel method. Six top ranked compounds that were not known to interact with ADH3 were tested in vitro, where two showed substrate activity (9-decen-1-ol and dodecyltetraglycol), two showed inhibition capacity (deoxycholic acid and doxorubicin) and two did not have any detectable effect. For the substrates, site specific interactions and calculated binding scoring energies were determined with an extended docking simulation including flexible side chains of amino acids residues. The binding scoring energies correlated well with the logarithm of the substrates kcat over Km values. Furthermore, with these computational and experimental data three different lines for specific inhibitors for ADH3 are suggested: fatty acids, glutathione analogs and in addition deoxycholic acids.
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| 2. |
- Michelatto, Debora de Paula, et al.
(författare)
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Functional and Structural Consequences of Nine CYP21A2 Mutations Ranging from Very Mild to Severe Effects
- 2016
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Ingår i: International Journal of Endocrinology. - : Hindawi Limited. - 1687-8337 .- 1687-8345.
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Tidskriftsartikel (refereegranskat)abstract
- We present the functional and structural effects of seven novel (p.Leu12Met, p.Arg16Cys, p.Ser101Asn, p.Ser202Gly, p.Pro267Leu, p.Gln389 Ala391del, and p.Thr450Met) and two previously reported but not studied (p.Ser113Phe and p.Thr450Pro) CYP21A2 mutations. Functional analyses were complemented with in silico prediction of mutation pathogenicity based on the recently crystallized human CYP21A2 structure. Mutated proteins were transiently expressed in COS-1 cells and enzyme activities towards 17-hydroxyprogesterone and progesterone were determined. Residual enzyme activities between 43% and 97% were obtained for p.Arg16Cys, p.Ser101Asn, p.Ser202Gly, p.Pro267Leu, and p.Thr450Met, similar to the activities of the well-known nonclassic mutations p.Pro453Ser and p.Pro482Ser, whereas the p.Leu12Met variant showed an activity of 100%. Conversely, the novel p.Ser113Phe, p. Gln389 Ala391del, and p.Thr450Promutations drastically reduced the enzyme function below 4%. The K-m values for all novel variants were in the same order of magnitude as for the wild-type protein except for p.The450Met. The maximum velocity was decreased for all mutants except for p.Leu12Met. We conclude that p. Leu12Met is a normal variant; the mutations p.Arg16Cys, p.Ser101Asn, p.Ser202Gly, p.Pro267Leu, and p.Thr450Met could be associated with very mild nonclassic CAH, and the mutations p.Ser113Phe, p.Gln389 Ala391del, and p.Thr450Pro are associated with classic CAH. The obtained residual activities indicated a good genotype-phenotype correlation.
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| 3. |
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| 4. |
- Östberg, Katarina, 1978-, et al.
(författare)
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Benefit transfer for environmental improvements in coastal areas : General versus Best-Fitting models
- 2013
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Ingår i: Canadian Journal of Agricultural Economics-Revue Canadienne D'Agroeconomie. - : John Wiley & Sons. - 0008-3976 .- 1744-7976. ; 61:2, s. 239-258
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Tidskriftsartikel (refereegranskat)abstract
- Recognizing the important policy task of securing the benefits from marine coastal waters subject to time and funding constraints has increased interest in benefit transfer (BT). However, many of the advances in BT recommended by researchers would be too costly to implement. This paper presents two choice experiment (CE) studies on marine areas in Sweden where respondents from local and distant populations were surveyed. BT for attributes relevant to the European Union's Water Framework Directive and the implementation of special consideration zones in marine areas were evaluated by equivalence tests. A comparison of the performance between a “general” BT model including only easily available socio-economic information and a statistically “best-fitting” model that requires the collection of more detailed information shows very similar results. Using a general model saves money and time since the information needed can be easily obtained from public databases and it does not lead to any significant reductions in accuracy or reliability. The issue of including socio-economic information in CE modeling for BT is important, since the model specification will determine the type of information that must be collected at the policy site; however, the results are inconclusive as to whether it improves BT or not.La reconnaissance de l'importante tâche politique visant à protéger les avantages tirés des eaux marines côtières, exposée à des contraintes de temps et de financement, suscite un intérêt accru pour le transfert d'avantages (TA). Toutefois, la mise en œuvre d'un bon nombre des percées en matière de TA recommandées par les chercheurs serait trop coûteuse. Dans le présent article, nous présentons deux études sur des zones marines de la Suède réalisées selon la méthode des choix multi-attributs et auxquelles ont participé des répondants provenant de populations locales et éloignées. Le TA dans le cas d'attributs figurant dans la Directive-cadre sur l'eau de l’Union européenne et la détermination de zones nécessitant une prise en compte particulière au sein des zones marines ont été évalués à l'aide de tests d'équivalence. Une comparaison de la performance du modèle de TA « général », qui comprend uniquement des données socio-économiques facilement obtenables, et de celle du modèle de TA « optimal », qui comprend une collecte de données détaillées, montre des résultats très similaires. L'utilisation du modèle général permet d'économiser du temps et de l'argent puisque l'information requise est facilement accessible dans les bases de données publiques, sans diminution significative de la précision ou de la fiabilité. La question d'inclure des données socio-économiques dans le modèle de choix multi-attributs pour le TA est importante puisque que la spécification du modèle déterminera le type de données qu'il faut collecter sur l'endroit visé par la politique. Toutefois, les résultats ne permettent pas d'indiquer si le TA est amélioré ou non.
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| 5. |
- Östberg, Katarina, et al.
(författare)
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Non-market valuation of the coastal environment - Uniting political aims, ecological and economic knowledge
- 2012
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Ingår i: Journal of Environmental Management. - : Elsevier BV. - 0301-4797 .- 1095-8630. ; 110, s. 166-178
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we examine the feasibility of using an approach for estimating Willingness-To-Pay for marine environmental improvements, based on a holistic, policy-determined scenario. Conducting valuation studies based on a policy-determined scenario is beneficial for decision-makers in terms of practical applicability but also for research in terms of e.g. data availability. Using a case study in two Swedish coastal areas, we examine whether respondents are able to understand and attach a monetary value to these types of scenarios. The tested scenarios are based on improving water quality according to the EU Water Framework Directive and reducing noise and littering according to standard-type measures in a Swedish archipelago setting. The results are promising, paving the ground for future valuation studies using this approach. However, there might be tradeoffs, since the use of scenarios like this require much preparation by researchers and much efforts by respondents. We recommend environmental managers to adopt this approach when possible, but to have these potential tradeoffs in mind. Mean monthly WTP per household for the water quality improvement scenario is estimated to 71 and 102 SEK1 in the two study areas, respectively. The corresponding numbers for the less noise and littering scenario are 38 and 46 SEK. Valuation of noise and littering in archipelago areas has previously not been very common, making these estimates especially important for marine policy.
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| 6. |
- Östberg, Linus J., et al.
(författare)
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Computational analysis of human medium-chain dehydrogenases/ reductases revealing substrate- and coenzyme-binding characteristics
- 2024
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Ingår i: Chemico-Biological Interactions. - : Elsevier. - 0009-2797 .- 1872-7786. ; 390
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Tidskriftsartikel (refereegranskat)abstract
- The medium-chain dehydrogenase/reductase (MDR) superfamily has more than 600,000 members in UniProt as of March 2023. As the family has been growing, the proportion of functionally characterized proteins has been falling behind. The aim of this project was to investigate the binding pockets of nine different MDR protein families based on sequence conservation patterns and three-dimensional structures of members within the respective families. A search and analysis methodology was developed. Using this, a total of 2000 eukaryotic MDR sequences belonging to nine different families were identified. The pairwise sequence identities within each of the families were 80-90 % for the mammalian sequences, like the levels observed for alcohol dehydrogenase, another MDR family. Twenty conserved residues were identified in the coenzyme part of the binding site by matching structural and conservation data of all nine protein families. The conserved residues in the substrate part of the binding pocket varied between the nine MDR families, implying divergent functions for the different families. Studying each family separately made it possible to identify multiple conserved residues that are expected to be important for substrate binding or catalysis of the enzymatic reaction. By combining structural data with the conservation of the amino acid residues in each protein, important residues in the binding pocket were identified for each of the nine MDRs. The obtained results add new positions of interest for the binding and activity of the enzyme family as well as fit well to earlier published data. Three distinct types of binding pockets were identified, containing no, one, or two tyrosine residues.
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| 7. |
- Östberg, Linus J
(författare)
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Computational exploration of the medium-chain dehydrogenase/reductase superfamily
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The medium-chain dehydrogenase/reductase (MDR) superfamily is a protein family with more than 170,000 members across all phylogenetic branches. In humans there are 18 representatives. The entire MDR superfamily contains many protein families such as alcohol dehydrogenase, which in mammals is in turn divided into six classes, class I–VI (ADH1–6). Most MDRs have enzymatical functions, catalysing the conversion of alcohols to aldehyde/ketones and vice versa, but the function of some members is still unknown. In the first project, a methodology for identifying and automating the classification of mammalian ADHs was developed using BLAST for identification and class-specific hidden Markov models were generated for identification. By using the developed methodology, multiple new mammalian ADH members were identified. Finally, the generation of a phylogenetic tree of the sequences showed the existence of a sixth class, ADH6, in most non-primate mammals, though the sequences are commonly misclassified as ADH5 or ADH1-like in the sequence databases. The second project focused on the study of mammalian ADH5, which has never been isolated as a native protein, and whose function is unknown. The first part of the project was the expression of ADH5 fusion proteins in E. coli and COS cells (human ADH5 with glutathione-S-transferase in E. coli and rat ADH5-green fluorescent protein in COS cells). The proteins were expressed, but had no activity with any traditional ADH substrates. The results also indicated potential problems with the stability of the protein. The continuation of the project was the analysis of the structure using computational methods. A structural model of ADH5 was generated using the homolog ADH1C as template. Molecular dynamics was subsequently used to study the properties of the model. Along with the structural analysis, extensive sequence analysis was also performed, identifying multiple positions that were unique for AHD5, e.g. Lys51 at the active site and Gly305 in the dimerinteracting region, which replace a highly conserved Pro found in ADH1–4. The combination of the structural simulations and the sequence analysis led to the conclusion that the lack of success in the isolation of ADH5 could potentially be explained by instabilities in the region involved in dimer formation, preventing the formation of the active dimers found in other ADHs. The function of ADH5 is therefore concluded to be different than that of other ADHs, but is as of yet still unknown. The final project focused on the study of a set of human MDRs, using a combination of analyses of the structures and sequences, leading to the development of theoretical models of the binding pockets in each of the proteins, pinpointing the important residues. The positions identified to be involved in the binding of the coenzyme NADP(H) were similar between the proteins and matched currently available information in the databases, as well as further residues. The residues involved in the binding of substrates varied between the proteins, and the analysis led to the identification of three different types of substrate binding.
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| 8. |
- Östberg, Linus J., et al.
(författare)
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Computational studies of human class V alcohol dehydrogenase - the odd sibling
- 2016
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Ingår i: BMC Biochemistry. - : Springer Science and Business Media LLC. - 1471-2091. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background: All known attempts to isolate and characterize mammalian class V alcohol dehydrogenase (class V ADH), a member of the large ADH protein family, at the protein level have failed. This indicates that the class V ADH protein is not stable in a non-cellular environment, which is in contrast to all other human ADH enzymes. In this report we present evidence, supported with results from computational analyses performed in combination with earlier in vitro studies, why this ADH behaves in an atypical way. Results: Using a combination of structural calculations and sequence analyses, we were able to identify local structural differences between human class V ADH and other human ADHs, including an elongated beta-strands and a labile a-helix at the subunit interface region of each chain that probably disturb it. Several amino acid residues are strictly conserved in class I-IV, but altered in class V ADH. This includes a for class V ADH unique and conserved Lys51, a position directly involved in the catalytic mechanism in other ADHs, and nine other class V ADH-specific residues. Conclusions: In this study we show that there are pronounced structural changes in class V ADH as compared to other ADH enzymes. Furthermore, there is an evolutionary pressure among the mammalian class V ADHs, which for most proteins indicate that they fulfill a physiological function. We assume that class V ADH is expressed, but unable to form active dimers in a non-cellular environment, and is an atypical mammalian ADH. This is compatible with previous experimental characterization and present structural modelling. It can be considered the odd sibling of the ADH protein family and so far seems to be a pseudoenzyme with another hitherto unknown physiological function.
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